RT Journal Article
SR Electronic
T1 The I<em>n</em> S<em>ilico</em> Genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 015578
DO 10.1101/015578
A1 Jason W. Sahl
A1 Stephen M. Beckstrom-Sternberg
A1 James S. Babic-Sternberg
A1 John D. Gillece
A1 Crystal M. Hepp
A1 Raymond K. Auerbach
A1 Waibhav Tembe
A1 David M. Wagner
A1 Paul S. Keim
A1 Talima Pearson
YR 2015
UL http://biorxiv.org/content/early/2015/02/20/015578.abstract
AB The identification and annotation of nucleotide variants, including insertions/deletions and single nucleotide polymorphisms (SNPs), from whole genome sequence data is important for studies of bacterial evolution, comparative genomics, and phylogeography. The in Silico Genotyper (ISG) represents a parallel, tested, open source tool that can perform these functions and scales well to thousands of bacterial genomes. ISG is written in Java and requires MUMmer (Delcher, et al., 2003), BWA (Li and Durbin, 2009), and GATK (McKenna, et al., 2010) for full functionality. The source code and compiled binaries are freely available from https://github.com/TGenNorth/ISGPipeline under a GNU General Public License. Benchmark comparisons demonstrate that ISG is faster and more flexible than comparable tools.